John Mackey, a founder of Whole Foods Market, took the helm as sole chief executive last year in a bid to single-handedly revive the upscale grocer’s fortunes.

On Wednesday, facing growing pressure from restless shareholders, he brought in reinforcements.

A month after an activist hedge fund took a stake in Whole Foods and began to agitate for change, the company unveiled a sweeping overhaul of its board, replacing five directors, naming a new chairwoman and bringing in a new chief financial officer. It also laid out plans to improve operations and cut costs.

The defensive maneuvering comes as Whole Foods, an organic foods pioneer that helped change the way Americans shop and eat, faces the greatest crisis of confidence in its 37-year history. It also underscores the growing influence of activist shareholders, who continue to press corporate executives.

“We pay attention to what our shareholders tell us,” Mr. Mackey said in an interview.

“We’ve been told for some time that we needed to address governance issues,” he said, adding that a main concern from shareholders was that the board was not independent enough.

Among those joining the Whole Foods board is Ronald Shaich, the founder, chairman and co-chief executive of Panera Bread Company. The others are Ken Hicks, a former chief executive of Foot Locker; Joe Mansueto, the founder and chairman of Morningstar; Sharon McCollam, a former chief financial officer of Best Buy; and Scott Powers, a former vice president of State Street Corporation.

Gabrielle Sulzberger, a private equity executive, will become the company’s chairwoman, Whole Foods said in a statement. Ms. Sulzberger is married to Arthur O. Sulzberger Jr., the chairman and publisher of The New York Times. John B. Elstrott Jr., who has served as chairman of the Whole Foods board since 2009, will step down.

Keith Manbeck, a former vice president of Kohl’s, will become the company’s new chief financial officer.

The moves by Whole Foods came after Jana Partners, an $8.5 billion hedge fund, announced a major investment and proposed four nominees to the company’s board.

Neuberger Berman, another major shareholder, has also pushed for change at Whole Foods over the past year, at one point even turning to activist hedge funds for help.

Jana went public with its fight against Whole Foods last month. Its targets included customer service and brand development at the company, which has faced added competition from traditional grocers in recent years.

The hedge fund, arguing that the board was stale and in need of fresh blood, proposed a slate of directors that included Glenn Murphy, a former chief executive of Gap Inc., and Mark Bittman, a former food columnist for The New York Times. The potential directors bought their own stakes in the company.

Whole Foods tried to broker a peace with Jana, offering to accept two of the hedge fund’s nominees if Jana would refrain from publicly agitating for change for two years. Jana refused, a spokesman for the hedge fund said.

On Wednesday, Whole Food unveiled its own new picks for the board, foreshadowing what could be a showdown with some shareholders.

“If Jana wants to have their own directors on the board, then they ought to be willing to sign a cooperation agreement,” Mr. Mackey said.

Jana, for its part, said it wanted to remain nimble rather than strike a compromise with the company.

“We decided we’d rather keep all options on the table,” the Jana spokesman said in a statement. “Now we’ll be waiting to see if the newly reconstituted board can show a real commitment to fixing the operations at Whole Foods and pursuing all avenues to shareholder value creation.”

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Whole Foods is replacing several of the company’s directors and naming a new chairman.CreditJohn Taggart for The New York Times

Whole Foods detailed the changes as it announced quarterly earnings and subjected its financial health to the market’s microscope. Sales for the quarter met expectations, but the company pared back its forecast for earnings this year.

The Whole Foods brand was once synonymous with organic and natural foods, and the company staked its reputation on a culture of healthy eating and living. It stood out for offering fresh, local produce, but its products came with a hefty price tag, earning the grocer the nickname “whole paycheck” among some shoppers.

Whole Foods faces fierce competition and has been forced to slash prices as national retailers like Costco, Safeway and Walmart have begun offering their own organic produce and kitchen staples.

Wall Street started to lose faith in Whole Foods amid the shifting landscape, and the company’s shares slumped, although they have regained some of the lost ground since Jana announced its investment.

Whole Foods pledged on Wednesday to accelerate a planned customer loyalty program, after shareholders, including Jana and Neuberger Berman, had criticized it for being slow to adopt one. It also said it would cut $300 million in additional costs over the next four years.

And the grocer told investors that it would buy back $1.25 billion in shares.

But some shareholder demands remain. Neuberger Berman sent a letter to the board last week noting its concern that employees would be “distracted from their primary responsibilities” amid the flurry of public pressure. Neuberger Berman, which manages $267 billion for pension funds, sovereign wealth funds and individuals, urged Whole Foods to consider “possible strategic mergers, partnerships, joint ventures, alliances” in addition to making internal investments.

It was the second time that Neuberger Berman had sent a letter to the Whole Foods board. A month after its first letter, in September, the company announced a series of management changes.

Those changes included the elimination of the company’s co-chief executive structure and the appointment of Mr. Mackey as the sole chief executive. Walter Robb, the previous co-chief executive, continued to serve on the board. Whole Foods also brought Mary Ellen Coe, the vice president for sales and product operations at Google, onto the board. And it announced that Glenda Flanagan, the chief financial officer, would retire at the end of 2017.

In a statement on Wednesday, Neuberger Berman said, “We look forward to understanding the new board’s sense of urgency and timeline in assessing all strategic opportunities to maximize shareholder value.”

A version of this article appears in print on , on Page B1 of the New York edition with the headline: Whole Foods, Under Duress, Shuffles Board. Order Reprints | Today’s Paper | Subscribe